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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins

Fig. 4

Structural and Molecular Dynamics of W67F and W67F-L105W mutants. a Cartoon of 2IFW showing I51 (purple) at the start of a β-sheet as well as W67 (yellow) and E69 (cyan) relative to catalytic Q53. b Cartoon of 2IFW detailing the π–π stack between W67 (yellow) and PSA211 from the transition state inhibitor. c Cartoon of 2IFW showing π–π stacking (green licorice) and salt bridge (orange licorice) between eqolisin and transition state inhibitor. d Distance and its running average (over 5 ns, smoother solid line) for the π–π stacking of residue 67 with the inhibitor PSA211 phenyl ring in the WT, the W67F and L105W mutants as well as the W67F-L105W double mutant as determined by molecular dynamics simulation (e) Distance between D57@Og and LYS209@Hz in the WT, the W67F and L105W mutants as well as the W67F-L105W double mutant as determined by molecular dynamics simulation

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BMC Bioinformatics

ISSN: 1471-2105

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